text: /**
   * The MIT License (MIT)
   * Copyright (c) 2016-2017 Intel Corporation
   *
   * Permission is hereby granted, free of charge, to any person obtaining a copy of
   * this software and associated documentation files (the "Software"), to deal in
   * the Software without restriction, including without limitation the rights to
   * use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
   * the Software, and to permit persons to whom the Software is furnished to do so,
   * subject to the following conditions:
   *
   * The above copyright notice and this permission notice shall be included in all
   * copies or substantial portions of the Software.
   *
   * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
   * FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
   * COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
   * IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
  
  #ifndef GT_COMMON_H
  #define GT_COMMON_H
  
  #include "headers.h"
  #include "profiling.h"
  
  #include "vcf.h"
  
  #define CHECK_MISSING_SAMPLE_GIVEN_REF(REF) (((REF).size() == 0) || ((REF)[0] == '$'))
  #define CHECK_UNINITIALIZED_SAMPLE_GIVEN_REF(REF) ((REF).size() == 0 || ((REF) == ""))
  #define CHECK_IN_THE_MIDDLE_REF(REF) ((REF)[0] == 'N')
  extern std::string g_vcf_NON_REF;
  extern std::string g_vcf_SPANNING_DELETION;
  inline bool IS_NON_REF_ALLELE(const std::string& allele) {
    return allele.length() > 0 && ((allele)[0] == '&');
  }
  
  inline bool IS_NON_REF_ALLELE(const char allele_char) {
    return allele_char == '&';
  }
  
  #define TILEDB_NON_REF_VARIANT_REPRESENTATION "&"
  #define TILEDB_ALT_ALLELE_SEPARATOR "|"
  #define MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED 50u
  #define MAX_GENOTYPE_COUNT ((unsigned)INT32_MAX) //this is likely larger than what can be handled by the VCF format
  #define DEFAULT_COMBINED_VCF_RECORDS_BUFFER_SIZE 1048576u
  
  #define UNDEFINED_ATTRIBUTE_IDX_VALUE 0xFFFFFFFFu
  #define UNDEFINED_NUM_ROWS_VALUE 0xFFFFFFFFFFFFFFFFull
  #define UNDEFINED_UINT64_T_VALUE 0xFFFFFFFFFFFFFFFFull
  
  extern std::unordered_map<std::type_index, int> g_variant_field_type_index_to_tiledb_type;
  extern std::unordered_map<std::type_index, int> g_variant_field_type_index_to_bcf_ht_type;
  extern std::vector<std::type_index> g_tiledb_type_to_variant_field_type_index;
  
  extern std::string g_tmp_scratch_dir;
  
  extern const char* g_json_indent_unit;
  
  #endif
  